Package Bio :: Package Rebase
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Package Rebase

source code

This module provides code to work with files from Rebase. http://rebase.neb.com/rebase/rebase.html

Classes: Record Holds rebase sequence data. Iterator Iterates over sequence data in a rebase file. Dictionary Accesses a rebase file using a dictionary interface. RecordParser Parses rebase sequence data into a Record object.

_Scanner Scans a rebase-format stream. _RecordConsumer Consumes rebase data to a Record object.

Functions: index_file Index a FASTA file for a Dictionary.

Classes [hide private]
  Record
Holds information from a FASTA record.
  Iterator
Returns one record at a time from a Rebase file.
  Dictionary
Accesses a rebase file using a dictionary interface.
  RecordParser
Parses FASTA sequence data into a Record object.
  _Scanner
Scans a rebase file.
  _RecordConsumer
Consumer that converts a rebase record to a Record object.
Functions [hide private]
 
index_file(filename, indexname, rec2key=None)
index_file(filename, ind/exname, rec2key=None)
source code
Variables [hide private]
  __warningregistry__ = {('Bio.Rebase was deprecated, as it does...
  xml_support = 1
Function Details [hide private]

index_file(filename, indexname, rec2key=None)

source code 

index_file(filename, ind/exname, rec2key=None)

Index a rebase file. filename is the name of the file. indexname is the name of the dictionary. rec2key is an optional callback that takes a Record and generates a unique key (e.g. the accession number) for the record. If not specified, the sequence title will be used.


Variables Details [hide private]

__warningregistry__

Value:
{('Bio.Rebase was deprecated, as it does not seem to be able to parse \
recent HTML files from Rebase. If you want to continue to use this mod\
ule, please get in contact with the Biopython developers at biopython-\
dev@biopython.org to avoid permanent removal of this module from Biopy\
thon',
  <type 'exceptions.DeprecationWarning'>,
  27): 1}